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Pull requests: fulcrumgenomics/fgbio

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Pull requests list

feat: add a a read name filtering writer to the API
#1037 opened Feb 28, 2025 by nh13 • Draft
1
feat: a default base quality may be provided in consensus callers whe… enhancement
#1032 opened Feb 20, 2025 by nh13 • Draft
1
@nh13
2
feat: add optical duplicate tagging to GroupReadsByUmi
#1029 opened Feb 16, 2025 by yfarjoun • Draft
1
@yfarjoun
1
feature/cached-aligner bugfix
#1024 opened Jan 30, 2025 by TimD1 Loading…
1
WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne • Draft
1
Added some tests to the longestDinuc to cover more edge cases
#1007 opened Aug 21, 2024 by yfarjoun Loading…
@nh13
2
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989 opened May 20, 2024 by nh13 Loading…
8
Add DownsampleVcf tool
#974 opened Mar 29, 2024 by TedBrookings Loading…
@nh13
28
GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads
#964 opened Jan 30, 2024 by nh13 Loading…
1
@tfenne
17
Bug Fix - SamRecordClipper.numBasesExtendingPastMate bug help wanted
#937 opened Sep 20, 2023 by JoeVieira Loading…
2
Add option to maintain N in umi needs review
#907 opened Apr 7, 2023 by JoeVieira Loading…
@nh13
12
Yf coverage unifier
#891 opened Dec 11, 2022 by yfarjoun Loading…
@yfarjoun
Add an option to skip the mate cigar in EstimateRnaSeqInsertSize needs review
#871 opened Aug 16, 2022 by nh13 Loading…
@nh13 @clintval
5
Add an option to sort by sequence role in CollectAlternateContigNames needs review
#868 opened Jul 31, 2022 by nh13 Loading…
@nh13
5
Expose chunkSize parameter in CallDuplexConsensusReads
#867 opened Jul 30, 2022 by mjhipp Loading…
@tfenne
22
Remove VariantContexts from most fgbio tools
#836 opened Apr 29, 2022 by kstromhaug Loading…
1
Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests
#832 opened Apr 25, 2022 by kstromhaug Loading…
3
Add metric builder and sorter
#826 opened Apr 20, 2022 by nh13 Loading…
@clintval
9
Remove uses of VariantContextSetBuilder in all unit tests
#819 opened Mar 28, 2022 by kstromhaug • Draft
1
Add a github action for generating tool and metrics docs
#811 opened Mar 10, 2022 by nh13 • Draft
@clintval
1
Add scala implementations for some SamRecord methods
#809 opened Mar 10, 2022 by nh13 Loading…
@nh13
33
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne • Draft
Add an entrypoint to SamSource for bytes of SAM/BAM/CRAM
#760 opened Jan 13, 2022 by clintval Loading…
6
Command line tool to produce and print pairwise alignments.
#739 opened Nov 11, 2021 by tfenne Loading…
@tfenne
5
Add source classes for BED and generic Interval types
#665 opened Feb 28, 2021 by clintval Loading…
@tfenne
2
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